The Prime Minister's bodyguards directed traffic around a high rise close to collapse, slips caused traffic chaos and homes were evacuated due to flooding as Wellington was hit by storms and aftershocks yesterday.

Just a day after Monday's magnitude 7.5 quake, the Capital was inundated with more rain in 24 hours than it would usually receive in a month.

The city usually only receives 74.8mm in November, Niwa said, but according to MetService, Wainuiomata recorded 109.5mm of rain in the 24 hours to yesterday afternoon.

Lower Hutt received 94.2mm, Porirua about 80mm, and Wellington 59.6mm at Kelburn.

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And after more than a day of aftershocks - 1212 last night, since the large quake hit early Monday morning - the weather caused chaos across the region.

Between 8am and 7.30pm, five strong aftershocks rattled the country - the most severe being a 4km deep 5.8 magnitude quake which hit 15km east of Seddon just after 2.30pm.

Slips and flooding saw closures on State Highways 1, 2 and 58, cutting the city off to traffic and marooning workers.

In the morning, motorists were stranded on SH2 between Ngauranga and Petone where floodwaters up to half a metre deep caused the road to resemble a river.

A stretch of about 12 houses were evacuated along the Lower Hutt's Riverside Dr, after Waiwhetu Stream flooded, with three people needing assistance from authorities.

Residents were able to return home yesterday.

KiwiRail's Capital Connection was cancelled overnight, and commuter buses, trains and ferries were severely disrupted.

Just before 5pm yesterday, fire crews arrived at an office block at 61 Molesworth St after they were contacted by an engineer with concerns about a structural beam "like a broken bone".

A section of Molesworth St that includes Wellington Cathedral of St Paul, the National Library and NZ Rugby headquarters and the Thai embassy has been cordoned off, with emergency workers warning the building is at significant risk of collapse.

Members of the Prime Minister's protection detail helped with traffic control.

Fire region manager Brendan Nally said it was unlikely office workers and residents in buildings within the cordoned-off areas would be let back in yesterday.

"We have a clear structural failure. What's caused that will be determined later.

"The clear structural failure is a major beam.

"It looks somewhat like a broken bone in the leg. It is fractured through. It is a major supporting beam. It is up above the fifth floor."

Statistics House, owned by Greater Wellington Regional Council and the Manawatu-Wanganui Regional Council company CentrePort, was severely damaged after Monday's quake.

Yesterday, Statistics New Zealand chief executive Liz MacPherson said she was grateful the 500 staff were not inside when it hit at 12.03am on Monday.

The building, which is only 11 years old, suffered serious structural damage.

In a video statement, MacPherson asked: "How is it a building as new as Stats House with the code rating that it had - could suffer this sort of damage?"

An update for Statistics NZ employees from Government Statistician and Chief Executive Liz MacPherson:

Posted by Stats NZ on Monday, 14 November 2016

Many other buildings remained shut yesterday - Greater Wellington Regional Council was badly damaged and car parks at Clifton and Courtenay Central, the James Smith building, Lombard and TSB/Queens Wharf were awaiting assessment.

Inner city roads were also closed due to risks posed from falling debris.

Shelly Bay Rd in Maupuia was closed due to a major slip south of the old Air Force base, which would likely take two to three days to clear.

One lane of Featherston St, Wellington Central, was closed as well as nearby Panama St, Brandon St, and Waring Taylor St.

The corner of Lambton Quay and Brandon St (Harbour City Centre) was also cordoned because of the risk of falling glass.

Cordons are in place until further notice due to the risk of falling debris.

Pipitea St in Thorndon, between Murphy St and Moturoa St, was cordoned for the same reason.

Today's forecast for the capital is a bit more subdued, with clouds, fine breaks and a few showers, clearing in the afternoon.

In some areas, northwesterlies will rise to gales in exposed places and more rain will develop in the evening.